Are you using JDK16 or Diablo JDK16? I have heard of people having trouble with the latter. Not that I believe that is the cause of this particular issue. Please post more of the error.

Diablo JDK16 is the binary set, which is a pre-requisite for installed JDK16 (which is compiled from source.) I firmly advise, based solely on personal experience, installing /usr/ports/java/jdk16 prior to installing eclipse or eclipse-devel.

All that said, this seems to be a problem building GNOME stuff, not Java stuff anyways. Once more errors are posted, we can come up with some advice.

Assuming you have a cvsup file for your ports... I'll call it ${CVSUPFILE}
If you don't have one, go ahead and copy /usr/share/examples/cvsup/ports-supfile somewhere, and edit it as appropriate.
Try running this set of commands, as root:

Those commands will completely blow away the offending ports, and get the latest versions of them from the CVSUP mirror you select in your ${CVSUPFILE} (there's a mirror list on www.freebsd.org if you need one to select one near to you.)

Once those have run, go back to trying to install Eclipse. Let us know how it goes. If it still doesn't work after that, it'll be time to contact the gnome team and/or file a pr, most likely.

If you ran the commands in my code block in that exact order, and still have the same results, then you should probably send-pr about it. Remember that this issue has nothing to do with Eclipse, and is a problem with the libgnome port, not Eclipse. The problem is simply with a dependency for Eclipse. Going to the Eclipse folks will yield no results. Instead, go to the FreeBSD GNOME folks via a send-pr. You may want to quote the URL to this thread in the PR text so that anyone looking over it can see what you've already tried, as the advice I gave you is usually the first advice given to anyone with problems such as yours by a port maintainer.